It was a stark reminder that "evil does exist in the world", as President Obama put it in his Nobel peace prize acceptance speech. But the aftermath of the foiled Christmas Day attack is casting a shadow over his landmark promise for a "new beginning" with the Muslim world based on "mutual interest" and "mutual respect".

The president's response in the coming weeks and months will be critical in shaping a relationship tattered by US action after the September 11 attacks, seen as having disproportionately singled out and targeted Muslims.

Leading Muslim groups have already decried the new enhancements as "profiling" Muslims. Citizens of and passengers from 13 Muslim-majority nations and Cuba are now singled out for additional screening, such as body imaging scanners and full-body pat-downs – even if they have lived in places like the US for years.

Ruling over a nation still badly bruised by the September 11 attacks, the US president is playing more to his domestic audience than an international one for now. The thwarted bombing has dwarfed the Afghan debate – which saw critics thirsting for blood as Obama hunkered down for months before announcing his troop increase – because it hits much closer to home. Yet he must also be careful to avoid the same kind of backlash generated against Muslims after 9/11, an impact still felt today. Can he prevail over security hawks and retain his Obama-cool while making only the necessary changes?

This is not the time to overreact, which could burn already crumbling bridges with Muslim and Arab allies critical in the fight against militants. Rather, cool heads should prevail to craft a sober response to improve security and resilience against attacks. Only a weak nation could allow militants to change its very fabric.

That's a message Obama took to heart when he swore that "we will define the character of our country, not some small band of men intent on killing innocent men, women and children". The president also insisted he would make no policy changes that would curtail civil liberties or freedom of movement, saying "we will not succumb to a siege mentality".

Profiling, if indeed necessary, should not focus on race, ethnicity, nationality or creed but on criminal behaviour. Setting additional measures for people who fit in those easily identifiable criteria only simplifies the task for extremists, who can circumvent the system and exploit loopholes. Several weeks ago, few people would have raised an eyebrow at a young London-educated Nigerian from a prominent family. And for good reason.

Accused shoe bomber Richard Reid, like Abdulmutallab, boarded the plane he intended to blow up after buying a one-way ticket with cash and did not check any luggage. That is one of many red flags that should have caught the eye of intelligence and security officers. Making unverified assumptions and glossing over seemingly banal facts has scuttled countless investigations.

Faced with the same criticism that dogged his presidential campaign – that he is too inexperienced and too soft on terror – Obama, the anti-Bush, toughened his response in a tone more akin to his predecessor. "We are at war," he said. For all his soaring rhetoric and promises to turn the page on George W Bush's eight years in office, Obama has largely preserved the same policies.

Obama may have rejected using words like "war on terror" or "Islamofascism" and blunted some of Bush's harshest policies but a year into his presidency, he has retained military commissions, asserted state secrets privileges, expanded the use of unmanned drones to strike al-Qaida targets in Pakistan, as well as announced plans to hold dozens of terror suspects indefinitely without charge and triple the number of US troops in Afghanistan.

Last week, however, he moved away from blaming the watch list system set up under Bush for failing to flag the Nigerian accused of trying to set off explosives stitched into his underwear. With a White House very eager to move on, he took ownership of the problem, invoking Harry Truman's famous phrase and saying: "The buck stops with me."

The foiled attack has turned the spotlight on Yemen, long a base for al-Qaida. What seems evident is that a US counterterrorism effort focused overwhelmingly on Afghanistan and Pakistan has taken its eyes off the ball in other weak states that provide a vacuum for extremists to thrive.

Yemen, where the underwear bomber allegedly received training from an al-Qaida affiliate, faces multiple serious challenges, such as dwindling oil reserves, a water shortage, a major insurgency in the north, secessionist movements in the south and high unemployment hitting its young population.

The botched attack has also dealt yet another blow to Obama's plans to shutter the US military prison at Guantánamo reviled around the world, a promise that also falls under his outreach to Muslims.

Yemeni detainees account for nearly half of the 198 prisoners who still linger there. But the president has announced a halt on transferring any Yemeni prisoners cleared for release back to their home country, out of fear they could return to the fight in the wake of Abdulmutallab's attempted suicide bombing.

In times of war, the US is not alone in having put aside hard-fought civil liberties. Let's hope that this time, it won't last long.